PDB-5ggv: CTLA-4 in complex with tremelimumab Fab

ID or keywords:

Entry

Database: PDB / ID: 5ggv

Title

CTLA-4 in complex with tremelimumab Fab

Components

Cytotoxic T-lymphocyte protein 4Cytotoxic T cell
heavy chain
light chain

Keywords

IMMUNE SYSTEM /

antibody

Function / homology

Function and homology information

protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway /

adaptive immune response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.998 Å

Authors

Heo, Y.S.

Citation

Journal: Nat Commun / Year: 2016
Title: Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy
Authors: Lee, J.Y. / Lee, H.T. / Shin, W. / Chae, J. / Choi, J. / Kim, S.H. / Lim, H. / Won Heo, T. / Park, K.Y. / Lee, Y.J. / Ryu, S.E. / Son, J.Y. / Lee, J.U. / Heo, Y.S.

History

Deposition	Jun 16, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ggv.cif.gz	234.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ggv.ent.gz	196.9 KB	Display	PDB format
PDBx/mmJSON format	5ggv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggv ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggv	HTTPS FTP

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Related structure data

Related structure data	5ggqC 5ggrC 5ggsC 5ggtC 5gguC C: citing same article (ref.)
Similar structure data	4z5r-5 4tsb-d 6svl-4 5x8l-1 4ttd-2 4tsc-d 4z5r-3 6nmu-1 4z5r-8 4z5r-1 6uta-2 5tz2-d 5ggs-1 1nbz-d 5ggs-2 4z5r-4 6ye3-2 6ye3-1 5vjo-1 4yc2-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #128 - Aug 2010 Interferons similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

L: light chain

H: heavy chain

Y: Cytotoxic T-lymphocyte protein 4

62.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	131.559, 48.207, 118.714
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	Y-246- HOH

#1: Antibody	light chain / Mass: 23406.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody	heavy chain Mass: 25951.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein	Cytotoxic T-lymphocyte protein 4 / Cytotoxic T cell / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4 Mass: 13510.340 Da / Num. of mol.: 1 / Fragment: UNP residues 36-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P16410
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate tribasic dihydrate, pH 5.6, 12% PEG4,000, 100 mM NaCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.99→50 Å / Num. obs: 51708 / % possible obs: 99.3 % / Redundancy: 6.6 % / Net I/σ(I): 41.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.998→31.696 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8

	R_factor	Num. reflection	% reflection
R_free	0.2144	2634	5.09 %
R_work	0.181	-	-
obs	0.1827	51708	99.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.998→31.696 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4234	0	0	432	4666

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4337
X-RAY DIFFRACTION	f_angle_d	1.081	5896
X-RAY DIFFRACTION	f_dihedral_angle_d	13.423	1550
X-RAY DIFFRACTION	f_chiral_restr	0.045	666
X-RAY DIFFRACTION	f_plane_restr	0.005	755

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9979-2.0342	0.2481	161	0.2043	2446	X-RAY DIFFRACTION	97
2.0342-2.0734	0.238	132	0.1991	2535	X-RAY DIFFRACTION	99
2.0734-2.1157	0.2268	134	0.1869	2562	X-RAY DIFFRACTION	99
2.1157-2.1617	0.2455	127	0.1856	2577	X-RAY DIFFRACTION	100
2.1617-2.2119	0.2451	123	0.1741	2551	X-RAY DIFFRACTION	99
2.2119-2.2672	0.2176	142	0.1843	2563	X-RAY DIFFRACTION	100
2.2672-2.3285	0.2027	151	0.1815	2541	X-RAY DIFFRACTION	100
2.3285-2.397	0.2244	135	0.1883	2574	X-RAY DIFFRACTION	99
2.397-2.4743	0.2104	119	0.1947	2565	X-RAY DIFFRACTION	99
2.4743-2.5627	0.2366	145	0.1976	2578	X-RAY DIFFRACTION	100
2.5627-2.6653	0.2642	145	0.1956	2572	X-RAY DIFFRACTION	100
2.6653-2.7865	0.2588	137	0.1904	2577	X-RAY DIFFRACTION	100
2.7865-2.9334	0.2427	153	0.1906	2566	X-RAY DIFFRACTION	100
2.9334-3.117	0.2496	155	0.1898	2598	X-RAY DIFFRACTION	100
3.117-3.3574	0.2044	142	0.1856	2602	X-RAY DIFFRACTION	100
3.3574-3.6948	0.1942	159	0.1743	2621	X-RAY DIFFRACTION	100
3.6948-4.2284	0.2001	118	0.1656	2660	X-RAY DIFFRACTION	100
4.2284-5.3232	0.1612	133	0.1556	2675	X-RAY DIFFRACTION	99
5.3232-31.6998	0.2234	123	0.1948	2711	X-RAY DIFFRACTION	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.6309	1.2649	-0.7529	5.5492	-2.9532	4.3291	0.1501	0.5526	-0.0102	-0.7759	0.0484	0.3487	0.292	-0.3787	-0.173	0.357	0.0986	-0.0962	0.4182	-0.0122	0.2387	17.6158	39.4938	88.5176
2	1.9055	-0.4387	-0.3604	2.4439	-0.6061	3.199	0.158	0.4136	0.1679	-0.36	0.0014	0.2896	-0.038	-0.2781	-0.147	0.2134	0.0546	-0.045	0.2052	0.0128	0.1907	20.0466	38.959	97.6611
3	1.197	-0.5099	-0.8228	1.2266	-0.6572	3.2521	0.1978	0.301	0.1534	-0.237	-0.0568	0.2343	-0.3728	-0.2315	-0.1382	0.2289	0.0413	-0.0487	0.2258	0.0145	0.2178	18.7131	42.1047	97.9052
4	0.4324	0.1053	-1.502	0.0159	-0.6076	4.7544	0.0196	0.0969	0.1032	-0.0729	0.0993	0.0041	-0.4496	-0.5412	-0.0506	0.4927	0.1026	-0.0073	0.4282	0.0665	0.2399	24.6759	46.4148	76.3737
5	3.0007	-1.4956	-0.2331	2.756	-0.3488	3.307	-0.1946	0.2135	-0.0381	-0.0578	0.2499	-0.1306	-0.0456	0.3826	-0.0676	0.4264	-0.035	0.0079	0.4762	-0.052	0.1831	41.7501	35.5796	67.2132
6	0.4349	0.2652	-0.018	1.7732	3.4149	7.1694	0.0563	0.1108	-0.0645	0.0583	-0.0068	0.0453	0.4522	-0.6154	-0.019	0.4118	0.0095	0.0239	0.4007	-0.0288	0.1955	38.1766	26.9883	67.2611
7	3.2475	-1.2616	-1.3938	3.0143	0.3058	2.5933	-0.1641	0.3866	-0.1094	0.2411	0.1809	-0.2267	0.3026	0.311	-0.05	0.4021	0.0323	-0.0164	0.4805	-0.0458	0.2091	40.4229	34.6356	67.7487
8	7.6936	-2.8501	-1.2925	3.1039	1.0438	0.8786	0.3394	1.249	-0.1025	-0.5917	-0.2014	-0.0526	-0.3922	0.0675	-0.143	0.4698	-0.0549	-0.0012	0.5318	-0.0187	0.2121	36.4147	36.5061	58.6786
9	2.3922	0.0109	-0.686	4.0169	1.9493	3.539	-0.0208	0.095	0.1607	0.3305	0.385	-0.9737	0.2739	0.6012	-0.3519	0.1704	0.0468	-0.0202	0.2935	-0.0307	0.267	44.2081	31.9312	102.7101
10	1.452	-0.0629	0.2012	1.6249	0.0169	1.9905	0.0676	0.0732	-0.0771	0.0041	0.007	-0.098	0.1184	0.1108	-0.0793	0.1629	0.0279	-0.0123	0.1296	-0.0148	0.1941	32.9259	32.1181	108.3656
11	1.6855	-0.3806	0.2392	6.3716	4.459	9.1553	0.0981	0.0675	-0.261	0.3909	-0.0692	-0.106	0.8995	0.0877	0.0049	0.2026	0.0308	0.0022	0.1426	-0.0023	0.2488	35.701	25.3984	109.7795
12	2.0844	-1.5043	-1.4234	2.3372	-0.2532	2.1946	0.0944	0.2493	-0.3508	-0.1148	-0.1812	0.1421	0.5974	-0.1112	0.0077	0.215	0.026	-0.0265	0.2011	-0.0391	0.3148	40.0117	25.1443	103.2624
13	4.6118	-1.5468	-3.7117	0.8774	1.2404	4.0077	0.0747	0.0365	0.088	-0.0091	-0.0524	0.0424	-0.0832	-0.0647	-0.045	0.1414	0.0091	-0.0065	0.1227	-0.0053	0.1831	25.4737	39.1615	109.6483
14	2.0568	-0.3584	-1.4397	1.4663	0.6901	3.1229	-0.098	0.3003	0.1461	-0.3456	0.2256	-0.1469	-0.1517	0.397	-0.1527	0.2639	-0.0695	-0.0273	0.3806	-0.0243	0.2617	46.2833	37.4342	80.5237
15	2.8534	-0.9556	0.351	3.075	-0.8919	2.8671	-0.2573	0.187	0.4405	-0.0894	0.1417	-0.4566	-0.3191	0.4188	0.0771	0.3154	-0.0598	-0.0257	0.4081	-0.0372	0.2433	47.1258	41.6452	77.8007
16	4.6364	-0.8895	2.1438	5.5324	-3.6334	2.1501	-0.2737	0.3252	0.432	0.3952	-0.2958	-1.3746	-1.1781	1.1744	0.2577	0.5355	-0.1764	-0.0603	0.5529	0.0198	0.5164	56.6062	44.7272	76.1131
17	3.976	-3.8826	-5.7857	2.0107	2.0127	1.9944	-0.1057	0.3647	-0.5109	-0.8285	-0.4508	1.3591	-0.0851	-0.4622	0.5368	0.3275	0.0114	-0.0916	0.4023	0.037	0.4757	6.3856	30.0654	113.1538
18	3.1905	-0.9078	-0.0592	5.2368	2.1781	4.3027	-0.0171	-0.002	-0.5315	0.3413	0.1388	0.0719	0.1505	-0.3701	-0.0182	0.2205	0.0064	0.0216	0.3475	0.0657	0.3845	3.3793	36.3428	128.3192
19	3.7341	-5.1824	-1.6942	7.3567	1.9535	4.52	0.0349	-0.074	-0.2125	-0.3126	-0.1577	0.3465	0.0544	-0.2906	0.1307	0.0952	-0.0022	-0.0385	0.2486	-0.003	0.2513	15.3613	31.5605	119.9463
20	2.0348	-0.8491	-0.1615	8.1418	-1.4229	3.7676	-0.1544	-0.2251	-0.1792	0.0721	-0.0353	-0.0596	0.0709	0.0797	0.1377	0.2317	0.0558	-0.04	0.262	0.0134	0.3271	17.8965	32.9387	125.1618
21	9.8235	-0.7042	0.6459	5.3358	-0.0731	2.033	-0.8186	-1.5487	-1.5702	0.631	0.1211	-0.9215	1.6466	-0.3002	0.6826	0.9554	0.0495	0.1399	0.6514	0.0841	0.8782	15.5373	25.2618	132.1474
22	2.5799	-0.3972	-0.0281	2.5895	0.4808	7.4621	-0.5994	-0.3368	-1.4053	0.2925	0.5148	0.4342	1.8956	-0.6546	0.1953	0.7831	-0.0784	0.179	0.5521	0.1792	0.7762	8.0555	25.3484	127.9409
23	3.9107	-0.9283	-0.7441	2.1266	0.9774	5.4984	-0.2569	-0.23	0.0633	0.8175	0.4928	-0.4879	0.3664	0.3461	-0.2226	0.2205	0.0573	-0.0685	0.3175	0.0252	0.3854	8.9595	38.9496	131.9743
24	2.1282	-3.7312	-1.931	2.2614	4.0201	2.8664	0.1003	-0.1245	0.006	-0.0631	-0.0401	0.0219	0.0014	-0.2886	-0.0466	0.1771	-0.0038	0.0098	0.259	0.0086	0.354	14.7659	31.5643	119.34
25	2.4821	-3.0683	-1.7211	5.3731	2.1717	2.998	-0.0002	-0.1217	0.0921	0.1999	0.1235	0.015	-0.0031	-0.2461	-0.1233	0.169	0.0039	-0.0168	0.2334	0.0096	0.2991	10.4435	36.3678	120.9544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 19 through 48 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 49 through 101 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 102 through 113 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 114 through 150 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 151 through 163 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 164 through 197 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 198 through 213 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 1 through 17 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 18 through 60 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 61 through 76 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 77 through 91 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 92 through 111 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 112 through 157 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 158 through 200 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 201 through 225 )
17	X-RAY DIFFRACTION	17	chain 'Y' and (resid 1 through 7 )
18	X-RAY DIFFRACTION	18	chain 'Y' and (resid 8 through 26 )
19	X-RAY DIFFRACTION	19	chain 'Y' and (resid 27 through 44 )
20	X-RAY DIFFRACTION	20	chain 'Y' and (resid 45 through 55 )
21	X-RAY DIFFRACTION	21	chain 'Y' and (resid 56 through 67 )
22	X-RAY DIFFRACTION	22	chain 'Y' and (resid 68 through 75 )
23	X-RAY DIFFRACTION	23	chain 'Y' and (resid 76 through 89 )
24	X-RAY DIFFRACTION	24	chain 'Y' and (resid 90 through 100 )
25	X-RAY DIFFRACTION	25	chain 'Y' and (resid 101 through 119 )

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